def test_top_contigs(self):
"""
Test top contigs from ref
"""
#ref_entry = ReferenceEntry.from_ref_dir(ref)
ref_entry = openReference(self.REFERENCE)
self.assertEqual(1, len(get_top_contigs_from_ref_entry(ref_entry, 2)))
def test_top_contigs(self):
"""
Test top contigs from ref
"""
#ref_entry = ReferenceEntry.from_ref_dir(ref)
ref_entry = openReference(self.REFERENCE)
self.assertEqual(1, len(get_top_contigs_from_ref_entry(ref_entry, 2)))
def test_get_consensus_table(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(ref_data, self._get_reference_entry())
self.assertEqual(5, len(table.columns))
self.assertEqual(self.CONTIG_ID, table.columns[0].values[0])
self.assertEqual(self.TEST_VALUES["contig_len"],
table.columns[1].values[0])
self.assertEqual(1, table.columns[2].values[0])
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
table.columns[3].values[0], places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
table.columns[4].values[0], places=2)
def make_variants_report(aln_summ_gff, variants_gff, reference, max_contigs_to_plot, report, output_dir, dpi=72, dumpdata=True):
"""
Entry to report.
:param aln_summ_gff: (str) path to alignment_summary.gff
:param variants_gff: (str) path to variants_gff
:param reference: (str) path to reference_dir
:param max_contigs_to_plot: (int) max number of contigs to plot
"""
_validate_inputs([('aln_summ_gff', aln_summ_gff),
('variants_gff', variants_gff),
('reference', reference)])
# reference entry & top contings
ref = openReference(reference)
top_contigs = get_top_contigs_from_ref_entry(ref, max_contigs_to_plot)
# extract gff data from files
ref_data, contig_variants = _extract_alignment_summ_data(
aln_summ_gff, top_contigs)
_append_variants_gff_data(ref_data, variants_gff)
# make report objects
table, atts = _get_consensus_table_and_attributes(ref_data, ref)
plotgroup = _create_variants_plot_grp(
top_contigs, contig_variants, output_dir)
rpt = Report(Constants.R_ID,
plotgroups=[plotgroup],
attributes=atts,
tables=[table],
dataset_uuids=(ReferenceSet(reference).uuid,))
rpt = spec.apply_view(rpt)
rpt.write_json(os.path.join(output_dir, report))
return rpt
def test_get_consensus_table(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(
ref_data, self._get_reference_entry())
self.assertEqual(5, len(table.columns))
self.assertEqual(self.CONTIG_ID, table.columns[0].values[0])
self.assertEqual(self.TEST_VALUES["contig_len"],
table.columns[1].values[0])
self.assertEqual(1, table.columns[2].values[0])
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
table.columns[3].values[0],
places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
table.columns[4].values[0],
places=2)
def test_get_consensus_attributes(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(ref_data, self._get_reference_entry())
self.assertEqual(5, len(attributes))
def __get_att_val(_id, atts):
for a in atts:
if a.id == _id:
return a.value
self.assertEqual(self.TEST_VALUES["contig_len"], __get_att_val("mean_contig_length", attributes))
self.assertAlmostEqual(
self.TEST_VALUES["bases_called"], __get_att_val("weighted_mean_bases_called", attributes), places=4
)
self.assertAlmostEqual(
self.TEST_VALUES["concordance"], __get_att_val("weighted_mean_concordance", attributes), places=4
)
self.assertAlmostEqual(
self.TEST_VALUES["coverage"], __get_att_val("weighted_mean_coverage", attributes), places=2
)
self.assertEqual(self.CONTIG_ID, __get_att_val("longest_contig_name", attributes))
def test_create_variants_plot_grp(self):
"""
Test that plotGroup of variants plots is created as expected
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 25)
ref_data, contig_variants = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)
plot_group = _create_variants_plot_grp(top_contigs, contig_variants, self._output_dir)
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
self._assert_image_file(plot_group.legend)
def test_extract_alignment_summ_data(self):
"""
Test the dicts returned from parsing the alignment_summary gff
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data, contig_variants = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
self.assertEqual(1, len(contig_variants))
def test_legend(self):
"""
Create the legend png
"""
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 25)
contig_variants = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[1]
ctgvar = None
for t in top_contigs:
ctgvar = contig_variants[t.header]
bars = _create_bars(ctgvar)
self.assertEqual(3, len(bars))
leg = _get_legend_file(bars, self._output_dir)
leg_path = op.join(self._output_dir, leg)
log.info('legend path: {l}'.format(l=leg_path))
self.assertTrue(op.exists(leg_path))
def test_append_variants_gff_data(self):
"""
Test that ERR information gets added to the ref_data dict
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY, top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_1"], results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_2"], results[ERR])
def test_extract_alignment_summ_data(self):
"""
Test the dicts returned from parsing the alignment_summary gff
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data, contig_variants = _extract_alignment_summ_data(
self.ALIGNMENT_SUMMARY, top_contigs)
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
self.assertEqual(1, len(contig_variants))
def test_create_variants_plot_grp(self):
"""
Test that plotGroup of variants plots is created as expected
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 25)
ref_data, contig_variants = _extract_alignment_summ_data(
self.ALIGNMENT_SUMMARY, top_contigs)
plot_group = _create_variants_plot_grp(top_contigs, contig_variants,
self._output_dir)
self.assertEqual(1, len(plot_group.plots))
self._assert_image_file(plot_group.thumbnail)
for plot in plot_group.plots:
self._assert_image_file(plot.image)
self._assert_image_file(plot_group.legend)
def test_get_consensus_attributes(self):
"""
Test the data in the table object and the attributes
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(0, results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
table, attributes = _get_consensus_table_and_attributes(
ref_data, self._get_reference_entry())
self.assertEqual(5, len(attributes))
def __get_att_val(_id, atts):
for a in atts:
if a.id == _id:
return a.value
self.assertEqual(self.TEST_VALUES["contig_len"],
__get_att_val('mean_contig_length', attributes))
self.assertAlmostEqual(self.TEST_VALUES["bases_called"],
__get_att_val('weighted_mean_bases_called',
attributes),
places=4)
self.assertAlmostEqual(self.TEST_VALUES["concordance"],
__get_att_val('weighted_mean_concordance',
attributes),
places=4)
self.assertAlmostEqual(self.TEST_VALUES["coverage"],
__get_att_val('weighted_mean_coverage',
attributes),
places=2)
self.assertEqual(self.CONTIG_ID,
__get_att_val('longest_contig_name', attributes))
def test_legend(self):
"""
Create the legend png
"""
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 25)
contig_variants = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[1]
ctgvar = None
for t in top_contigs:
ctgvar = contig_variants[t.header]
bars = _create_bars(ctgvar)
self.assertEqual(3, len(bars))
leg = _get_legend_file(bars, self._output_dir)
leg_path = op.join(self._output_dir, leg)
log.info('legend path: {l}'.format(l=leg_path))
self.assertTrue(op.exists(leg_path))
def test_append_variants_gff_data(self):
"""
Test that ERR information gets added to the ref_data dict
"""
# top_contigs = get_top_contigs(ref, 2)
top_contigs = get_top_contigs_from_ref_entry(
self._get_reference_entry(), 2)
ref_data = _extract_alignment_summ_data(self.ALIGNMENT_SUMMARY,
top_contigs)[0]
self.assertEqual(1, len(ref_data))
results = ref_data[self.CONTIG_ID]
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_1"], results[ERR])
_append_variants_gff_data(ref_data, self.VARIANTS_GFF)
self.assertEqual(self.TEST_VALUES["contig_len"], results[LENGTH])
self.assertEqual(self.TEST_VALUES["n_gff_err_2"], results[ERR])
